pione 0.5.0.alpha.2 → 0.5.0

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Files changed (65) hide show
  1. checksums.yaml +8 -8
  2. data/History.txt +2 -1
  3. data/example/DeferredChoiceWithPage/DeferredChoiceWithPage.pione +2 -5
  4. data/example/DeferredChoiceWithPage/{DefferredChoiceWithPage.pnml → DeferredChoiceWithPage.pnml} +0 -0
  5. data/example/DeferredChoiceWithPage/pione-package.json +2 -1
  6. data/example/FeatureExample/FeatureExample.pione +1 -1
  7. data/example/FeatureExample/pione-package.json +2 -2
  8. data/example/Fib/Fib.pione +9 -54
  9. data/example/Fib/FibN.pione +49 -0
  10. data/example/Interaction/Interaction.pione +6 -8
  11. data/example/Interaction/pione-package.json +6 -5
  12. data/example/LoopByTouch/LoopByTouch.pione +1 -3
  13. data/example/LoopByTouch/LoopByTouch.pnml +23 -6
  14. data/example/MakePair/scenario/case1/pione-scenario.json +28 -28
  15. data/example/MakePair/scenario/case2/pione-scenario.json +10 -10
  16. data/example/MakePair/scenario/case3/pione-scenario.json +26 -26
  17. data/example/OddSelector/OddSelector.pione +0 -1
  18. data/example/OddSelector/pione-package.json +2 -2
  19. data/example/OddSelector/scenario/pione-scenario.json +9 -9
  20. data/example/PegasusWMS/Merge/PegasusWMSMerge.pione +0 -1
  21. data/example/PegasusWMS/Merge/PegasusWMSMerge.pnml +2 -2
  22. data/example/PegasusWMS/Pipeline/PegasusWMSPipeline.pione +0 -1
  23. data/example/PegasusWMS/Split/PegasusWMSSplit.pione +0 -1
  24. data/example/ScoreAggregation/pione-package.json +3 -3
  25. data/example/ScoreAggregation/scenario/case1/pione-scenario.json +19 -19
  26. data/example/SelectRuleByParam/SelectRuleByParam.pione +5 -15
  27. data/example/SelectRuleByParam/pione-package.json +4 -0
  28. data/example/SequentialParameter/SequentialParameter.pione +0 -1
  29. data/example/SerialProcessing/A.pione +0 -1
  30. data/example/SerialProcessing/B.pione +0 -1
  31. data/example/SerialProcessing/SerialProcessing.pione +0 -1
  32. data/example/SerialProcessing/pione-package.json +2 -2
  33. data/example/SieveOfEratosthenes/CreateUndeterminedNumbers.pione +11 -0
  34. data/example/SingleParticlesWithRef/Create3dinfo.pione +36 -0
  35. data/example/SingleParticlesWithRef/Create3dinfo.pnml +5 -5
  36. data/example/SingleParticlesWithRef/Package.pione +3 -0
  37. data/example/SingleParticlesWithRef/SingleParticlesWithRef.pione +8 -91
  38. data/example/SingleParticlesWithRef/SingleParticlesWithRef.pnml +6 -6
  39. data/example/SingleParticlesWithRef/misc/{SingleParticlesWithRef.Display2.pione → SingleParticlesWithRef.Display2.pione.bak} +0 -0
  40. data/example/SingleParticlesWithRef/misc/{SingleParticlesWithRefFull.pione → SingleParticlesWithRefFull.pione.bak} +0 -0
  41. data/example/SingleParticlesWithRef/pione-package.json +20 -0
  42. data/example/WorkflowPatterns/07_StructuredSynchronizingMerge/StructuredSynchronizingMerge.pione +20 -46
  43. data/example/WorkflowPatterns/07_StructuredSynchronizingMerge/pione-package.json +19 -0
  44. data/example/WorkflowPatterns/12_MultipleInstancesWithoutSynchronization/MultipleInstancesWithoutSynchronization.pione +0 -1
  45. data/example/WorkflowPatterns/13_MultipleInstancesWithDesignTimeKnowledge/MultipleInstancesWithDesignTimeKnowledge.pione +0 -1
  46. data/example/WorkflowPatterns/14_MultipleInstancesWithRunTimeKnowledge/MultipleInstancesWithRunTimeKnowledge.pione +0 -1
  47. data/example/WorkflowPatterns/33_GeneralizedANDJoin/GeneralizedANDJoin.pione +0 -1
  48. data/example/WorkflowPatterns/38_GeneralSynchronizingMerge/GeneralSynchronizingMerge.pione +28 -68
  49. data/example/WorkflowPatterns/41_ThreadMerge/A.pione +24 -0
  50. data/example/WorkflowPatterns/41_ThreadMerge/A1.pione +14 -0
  51. data/example/WorkflowPatterns/41_ThreadMerge/ThreadMerge.pione +8 -31
  52. data/example/WorkflowPatterns/41_ThreadMerge/pione-package.json +21 -0
  53. data/example/WorkflowPatterns/42_ThreadSplit/ThreadSplit.pione +7 -7
  54. data/example/WorkflowPatterns/42_ThreadSplit/pione-package.json +19 -0
  55. data/lib/pione/command/pione-package-build.rb +2 -1
  56. data/lib/pione/lang/expr-parser.rb +1 -1
  57. data/lib/pione/lang/expr-transformer.rb +2 -0
  58. data/lib/pione/lang/type.rb +2 -2
  59. data/lib/pione/lang/variable.rb +8 -0
  60. data/lib/pione/pnml/compiler.rb +42 -23
  61. data/lib/pione/pnml/declaration-extractor.rb +16 -6
  62. data/lib/pione/pnml/pione-model.rb +18 -6
  63. data/lib/pione/pnml/ticket-instantiation.rb +2 -2
  64. data/lib/pione/version.rb +1 -1
  65. metadata +16 -7
data/example/MakePair/scenario/case2/pione-scenario.json CHANGED
@@ -2,21 +2,21 @@
2
2
  "ScenarioName": "case2",
3
3
  "ParamSet": null,
4
4
  "Inputs": [
5
- "input/9.i",
6
5
  "input/10.i",
7
- "input/11.i"
6
+ "input/11.i",
7
+ "input/9.i"
8
8
  ],
9
9
  "Outputs": [
10
- "output/perm-9-11.pair",
11
- "output/succ-10-11.pair",
12
- "output/perm-11-9.pair",
13
- "output/perm-10-11.pair",
10
+ "output/comb-10-11.pair",
14
11
  "output/comb-9-10.pair",
15
12
  "output/comb-9-11.pair",
16
- "output/comb-10-11.pair",
17
- "output/succ-9-10.pair",
18
- "output/perm-11-10.pair",
13
+ "output/perm-10-11.pair",
19
14
  "output/perm-10-9.pair",
20
- "output/perm-9-10.pair"
15
+ "output/perm-11-10.pair",
16
+ "output/perm-11-9.pair",
17
+ "output/perm-9-10.pair",
18
+ "output/perm-9-11.pair",
19
+ "output/succ-10-11.pair",
20
+ "output/succ-9-10.pair"
21
21
  ]
22
22
  }
data/example/MakePair/scenario/case3/pione-scenario.json CHANGED
@@ -2,42 +2,42 @@
2
2
  "ScenarioName": "case3",
3
3
  "ParamSet": null,
4
4
  "Inputs": [
5
- "input/9.i",
6
- "input/5.i",
5
+ "input/1.i",
7
6
  "input/3.i",
7
+ "input/5.i",
8
8
  "input/7.i",
9
- "input/1.i"
9
+ "input/9.i"
10
10
  ],
11
11
  "Outputs": [
12
- "output/perm-5-1.pair",
13
- "output/perm-7-1.pair",
12
+ "output/comb-1-3.pair",
13
+ "output/comb-1-5.pair",
14
+ "output/comb-1-7.pair",
15
+ "output/comb-1-9.pair",
16
+ "output/comb-3-5.pair",
17
+ "output/comb-3-7.pair",
18
+ "output/comb-3-9.pair",
19
+ "output/comb-5-7.pair",
20
+ "output/comb-5-9.pair",
21
+ "output/comb-7-9.pair",
22
+ "output/perm-1-3.pair",
23
+ "output/perm-1-5.pair",
24
+ "output/perm-1-7.pair",
25
+ "output/perm-1-9.pair",
14
26
  "output/perm-3-1.pair",
15
- "output/perm-9-5.pair",
27
+ "output/perm-3-5.pair",
16
28
  "output/perm-3-7.pair",
17
- "output/comb-3-9.pair",
18
29
  "output/perm-3-9.pair",
19
- "output/perm-7-9.pair",
20
- "output/perm-1-3.pair",
30
+ "output/perm-5-1.pair",
31
+ "output/perm-5-3.pair",
21
32
  "output/perm-5-7.pair",
22
- "output/perm-9-1.pair",
23
- "output/comb-1-9.pair",
24
- "output/perm-7-5.pair",
25
- "output/perm-1-7.pair",
26
- "output/comb-1-7.pair",
27
- "output/perm-1-5.pair",
28
- "output/comb-1-3.pair",
29
33
  "output/perm-5-9.pair",
34
+ "output/perm-7-1.pair",
30
35
  "output/perm-7-3.pair",
31
- "output/perm-9-7.pair",
32
- "output/perm-5-3.pair",
33
- "output/comb-5-7.pair",
34
- "output/perm-1-9.pair",
35
- "output/comb-3-7.pair",
36
- "output/perm-3-5.pair",
37
- "output/comb-7-9.pair",
36
+ "output/perm-7-5.pair",
37
+ "output/perm-7-9.pair",
38
+ "output/perm-9-1.pair",
38
39
  "output/perm-9-3.pair",
39
- "output/comb-1-5.pair",
40
- "output/comb-3-5.pair",
41
- "output/comb-5-9.pair"
40
+ "output/perm-9-5.pair",
41
+ "output/perm-9-7.pair"
42
42
  ]
43
43
  }
data/example/OddSelector/OddSelector.pione CHANGED
@@ -1,4 +1,3 @@
1
-
2
1
  Rule OddSelector
3
2
  input '*.i'.all
4
3
  output '*.res'.all
data/example/OddSelector/pione-package.json CHANGED
@@ -4,8 +4,8 @@
4
4
 
5
5
  ],
6
6
  "Documents": [
7
- "Package.pione",
8
- "OddSelector.pione"
7
+ "OddSelector.pione",
8
+ "Package.pione"
9
9
  ],
10
10
  "Scenarios": [
11
11
  "scenario"
data/example/OddSelector/scenario/pione-scenario.json CHANGED
@@ -2,22 +2,22 @@
2
2
  "ScenarioName": "from 1 to 10",
3
3
  "ParamSet": null,
4
4
  "Inputs": [
5
- "input/9.i",
6
- "input/2.i",
5
+ "input/1.i",
7
6
  "input/10.i",
8
- "input/5.i",
7
+ "input/2.i",
9
8
  "input/3.i",
9
+ "input/4.i",
10
+ "input/5.i",
11
+ "input/6.i",
10
12
  "input/7.i",
11
13
  "input/8.i",
12
- "input/1.i",
13
- "input/6.i",
14
- "input/4.i"
14
+ "input/9.i"
15
15
  ],
16
16
  "Outputs": [
17
- "output/3.res",
18
- "output/9.res",
19
17
  "output/1.res",
18
+ "output/3.res",
19
+ "output/5.res",
20
20
  "output/7.res",
21
- "output/5.res"
21
+ "output/9.res"
22
22
  ]
23
23
  }
data/example/PegasusWMS/Merge/PegasusWMSMerge.pione CHANGED
@@ -1,4 +1,3 @@
1
-
2
1
  Rule PegasusWMSMerge
3
2
  output 'binaries.txt'
4
3
  Flow
data/example/PegasusWMS/Merge/PegasusWMSMerge.pnml CHANGED
@@ -41,7 +41,7 @@ Created with Workflow PetriNet Designer Version 1.0 (woped.org)-->
41
41
  </place>
42
42
  <place id="p2">
43
43
  <name>
44
- <text>$DIRS := ("/bin" | "/usr/bin" | "/usr/local/bin").all</text>
44
+ <text>{DIRS: ("/bin" | "/usr/bin" | "/usr/local/bin").all}</text>
45
45
  <graphics>
46
46
  <offset x="100" y="290"/>
47
47
  </graphics>
@@ -56,7 +56,7 @@ Created with Workflow PetriNet Designer Version 1.0 (woped.org)-->
56
56
  </place>
57
57
  <place id="p1">
58
58
  <name>
59
- <text>$INDEX := 0.upto(2)</text>
59
+ <text>{INDEX: 0.upto(2)}</text>
60
60
  <graphics>
61
61
  <offset x="100" y="210"/>
62
62
  </graphics>
data/example/PegasusWMS/Pipeline/PegasusWMSPipeline.pione CHANGED
@@ -1,4 +1,3 @@
1
-
2
1
  Rule PegasusWMSPipeline
3
2
  output 'count.txt'
4
3
  Flow
data/example/PegasusWMS/Split/PegasusWMSSplit.pione CHANGED
@@ -1,4 +1,3 @@
1
-
2
1
  Rule PegasusWMSSplit
3
2
  output 'count.txt.*'.all
4
3
  Flow
data/example/ScoreAggregation/pione-package.json CHANGED
@@ -11,13 +11,13 @@
11
11
  "scenario/case1"
12
12
  ],
13
13
  "Bins": [
14
+ "bin/apply-template.rb",
15
+ "bin/histgram-graph.sh",
14
16
  "bin/mean-summary.rb",
15
17
  "bin/personal-bar-graph.sh",
16
18
  "bin/personal-pre-statistics.rb",
17
- "bin/apply-template.rb",
18
- "bin/total-statistics.rb",
19
19
  "bin/total-mean.rb",
20
- "bin/histgram-graph.sh"
20
+ "bin/total-statistics.rb"
21
21
  ],
22
22
  "Etcs": [
23
23
 
data/example/ScoreAggregation/scenario/case1/pione-scenario.json CHANGED
@@ -2,32 +2,32 @@
2
2
  "ScenarioName": "case1",
3
3
  "ParamSet": null,
4
4
  "Inputs": [
5
- "input/L.score",
6
- "input/O.score",
7
- "input/R.score",
8
- "input/F.score",
9
- "input/Y.score",
10
- "input/X.score",
11
- "input/H.score",
12
- "input/J.score",
5
+ "input/A.score",
13
6
  "input/B.score",
14
- "input/T.score",
15
7
  "input/C.score",
16
- "input/V.score",
17
- "input/P.score",
18
- "input/E.score",
19
- "input/I.score",
20
- "input/Q.score",
21
8
  "input/D.score",
22
- "input/W.score",
23
- "input/N.score",
24
- "input/A.score",
9
+ "input/E.score",
10
+ "input/F.score",
25
11
  "input/G.score",
26
- "input/U.score",
27
- "input/Z.score",
12
+ "input/H.score",
13
+ "input/I.score",
14
+ "input/J.score",
28
15
  "input/K.score",
16
+ "input/L.score",
29
17
  "input/M.score",
18
+ "input/N.score",
19
+ "input/O.score",
20
+ "input/P.score",
21
+ "input/Q.score",
22
+ "input/R.score",
30
23
  "input/S.score",
24
+ "input/T.score",
25
+ "input/U.score",
26
+ "input/V.score",
27
+ "input/W.score",
28
+ "input/X.score",
29
+ "input/Y.score",
30
+ "input/Z.score",
31
31
  "input/stat-template.erb"
32
32
  ],
33
33
  "Outputs": [
data/example/SelectRuleByParam/SelectRuleByParam.pione CHANGED
@@ -1,25 +1,16 @@
1
- .@ PackageName :: "SelectRuleByParam"
2
-
3
- Rule Main
1
+ Rule SelectRuleByParam
4
2
  output 'message.txt'
5
3
  param $NAME := "A"
6
4
  Flow
7
- case $NAME
5
+ case $NAME
8
6
  when "A"
9
- $RULE := A
7
+ rule A
10
8
  when "B"
11
- $RULE := B
9
+ rule B
12
10
  when "C"
13
- $RULE := C
11
+ rule C
14
12
  end
15
- rule RuleSelector {R: $RULE}
16
- End
17
13
 
18
- Rule RuleSelector
19
- output 'message.txt'
20
- param $R
21
- Flow
22
- rule $R
23
14
  End
24
15
 
25
16
  Rule A
@@ -39,4 +30,3 @@ Rule C
39
30
  Action
40
31
  echo "This is rule C." > {$O[1]}
41
32
  End
42
-
data/example/SelectRuleByParam/pione-package.json CHANGED
@@ -4,6 +4,7 @@
4
4
 
5
5
  ],
6
6
  "Documents": [
7
+ "Package.pione",
7
8
  "SelectRuleByParam.pione"
8
9
  ],
9
10
  "Scenarios": [
@@ -13,5 +14,8 @@
13
14
  ],
14
15
  "Bins": [
15
16
 
17
+ ],
18
+ "Etcs": [
19
+
16
20
  ]
17
21
  }
data/example/SequentialParameter/SequentialParameter.pione CHANGED
@@ -6,5 +6,4 @@ End
6
6
 
7
7
  Rule CreatedByParam
8
8
  output '{$N}.out'
9
- param $N := 1.upto(10)
10
9
  End
data/example/SerialProcessing/A.pione CHANGED
@@ -1,4 +1,3 @@
1
-
2
1
  Rule A
3
2
  output '*.a'.all
4
3
  Flow
data/example/SerialProcessing/B.pione CHANGED
@@ -1,4 +1,3 @@
1
-
2
1
  Rule B
3
2
  output '*.b'.all
4
3
  Flow
data/example/SerialProcessing/SerialProcessing.pione CHANGED
@@ -1,4 +1,3 @@
1
-
2
1
  Rule SerialProcessing
3
2
  output '*.b'.all
4
3
  output '*.a'.all
data/example/SerialProcessing/pione-package.json CHANGED
@@ -4,10 +4,10 @@
4
4
 
5
5
  ],
6
6
  "Documents": [
7
+ "A.pione",
7
8
  "B.pione",
8
9
  "Package.pione",
9
- "SerialProcessing.pione",
10
- "A.pione"
10
+ "SerialProcessing.pione"
11
11
  ],
12
12
  "Scenarios": [
13
13
  "scenario"
data/example/SieveOfEratosthenes/CreateUndeterminedNumbers.pione ADDED
@@ -0,0 +1,11 @@
1
+ Rule CreateUndeterminedNumbers
2
+ output '*.ud'.all
3
+ param $N := 2.upto($MAX)
4
+ Flow
5
+ rule CreateData
6
+ End
7
+
8
+ Rule CreateData
9
+ output '{$NAME}'
10
+ param $NAME := "{$N}.ud"
11
+ End
data/example/SingleParticlesWithRef/Create3dinfo.pione ADDED
@@ -0,0 +1,36 @@
1
+ Rule Create3dinfo
2
+ input '{$TARGET}.ref2d'
3
+ input '*.roi'
4
+ output '{$*}.fit'
5
+ output '{$*}.3dinfo'
6
+ Flow
7
+ rule ConvertPadToCorinfo
8
+ rule ConvertRoiToPad
9
+ rule ConvertCorinfoTo3dinfo
10
+ End
11
+
12
+ Rule ConvertPadToCorinfo
13
+ input '{$TARGET}.ref2d'
14
+ input '*.pad'
15
+ output '{$*}.corinfo'
16
+ output '{$*}.fit'
17
+ Action
18
+ mrcImageAutoRotationCorrelation -i {$*}.pad -r {$TARGET}.ref2d -O {$*}.corinfo -fit {$*}.fit -cor {$*}.cormap -n {$nROT} -m 18 -range {$ROTMIN} {$ROTMAX} -Iter 2 -nRot2 {$nRot2} -nRot1 {$nRot1} -nRot3 {$nRot3} 2> /dev/null
19
+ End
20
+
21
+ Rule ConvertRoiToPad
22
+ input '*.roi'
23
+ output '{$*}.pad'
24
+ Action
25
+ mrcImageWindowing -i {$*}.roi -o {$*}.mask -W 0.1 0.0 0.05 0.0 -m 18
26
+ mrcImagePad -i {$*}.mask -o {$*}.padtmp -W {$PAD_W} -H {$PAD_H} -m 3
27
+ mrcImageWindowing -i {$*}.padtmp -o {$*}.pad -W 0.1 0.0 0.1 0.0 -m 2
28
+ End
29
+
30
+ Rule ConvertCorinfoTo3dinfo
31
+ input '*.corinfo'
32
+ output '{$*}.3dinfo'
33
+ Action
34
+ awk '/Cor/ { print $7,$16,$2,$3,$4,$5,$9,$11,$12}' {$*}.corinfo | sort -r | sed -e s/.pad/.fit/ > {$*}.3dinfolst
35
+ head -n 1 {$*}.3dinfolst | awk '{print $2,$3,$4,$5,$6,$1}' > {$*}.3dinfo
36
+ End
data/example/SingleParticlesWithRef/Create3dinfo.pnml CHANGED
@@ -1,6 +1,6 @@
1
1
  <?xml version="1.0" encoding="UTF-8"?>
2
2
  <!--PLEASE DO NOT EDIT THIS FILE
3
- Created with Workflow PetriNet Designer Version 3.2.0 (woped.org)-->
3
+ Created with Workflow PetriNet Designer Version 1.0 (woped.org)-->
4
4
  <pnml>
5
5
  <net type="http://www.informatik.hu-berlin.de/top/pntd/ptNetb" id="noID">
6
6
  <place id="p7">
@@ -41,7 +41,7 @@ Created with Workflow PetriNet Designer Version 3.2.0 (woped.org)-->
41
41
  </place>
42
42
  <place id="p4">
43
43
  <name>
44
- <text>'*.pad'</text>
44
+ <text>'*.pad' #1</text>
45
45
  <graphics>
46
46
  <offset x="540" y="180"/>
47
47
  </graphics>
@@ -65,7 +65,7 @@ Created with Workflow PetriNet Designer Version 3.2.0 (woped.org)-->
65
65
  </place>
66
66
  <place id="p2">
67
67
  <name>
68
- <text>&lt;'{$TARGET}.ref2d'</text>
68
+ <text>&lt;'{$TARGET}.ref2d' #2</text>
69
69
  <graphics>
70
70
  <offset x="540" y="250"/>
71
71
  </graphics>
@@ -80,7 +80,7 @@ Created with Workflow PetriNet Designer Version 3.2.0 (woped.org)-->
80
80
  </place>
81
81
  <place id="p1">
82
82
  <name>
83
- <text>&lt;'*.roi'</text>
83
+ <text>&lt;'*.roi' #1</text>
84
84
  <graphics>
85
85
  <offset x="200" y="180"/>
86
86
  </graphics>
@@ -324,7 +324,7 @@ Created with Workflow PetriNet Designer Version 3.2.0 (woped.org)-->
324
324
  </arc>
325
325
  <toolspecific tool="WoPeD" version="1.0">
326
326
  <bounds>
327
- <position x="2" y="22"/>
327
+ <position x="2" y="25"/>
328
328
  <dimension x="1905" y="784"/>
329
329
  </bounds>
330
330
  <scale>100</scale>
data/example/SingleParticlesWithRef/Package.pione CHANGED
@@ -1,3 +1,6 @@
1
+ .@ PackageName :: "SingleParticlesWithRef"
2
+ .@ Entrance :: SingleParticlesWithRef
3
+
1
4
  #
2
5
  # Eos for 3D reconstrucion from 2D rois using 3D initail reference
3
6
  #